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<a href="CompNovoIdentification_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Sandro Andreotti $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Andreas Bertsch $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;</div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATION_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="comment">// OpenMS includes</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="CompNovoIdentificationBase_8h.html">OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationBase.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="comment">// stl includes</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;{</div>
<div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentification.html">   54</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> :</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a></div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;  {</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <a class="code" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a>();</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <a class="code" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> &amp; source);</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a>();</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    <a class="code" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> &amp; source);</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    <span class="keywordtype">void</span> getIdentifications(std::vector&lt;PeptideIdentification&gt; &amp; ids, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">PeakMap</a> &amp; exp);</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    <span class="keywordtype">void</span> getIdentification(<a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; CID_spec, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; ETD_spec);</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;</div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentification.html#acc1a3401cf6077f8a9625b25b51e0731">   87</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1CompNovoIonScoringBase.html#af7e67702d51d0eff4c3db8ea8763a59f">CompNovoIonScoringBase::IsotopeType</a> <a class="code" href="classOpenMS_1_1CompNovoIdentification.html#acc1a3401cf6077f8a9625b25b51e0731">IsotopeType</a>;</div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentification.html#a7b7c9d2595dd3328e664293d3fec5ef9">   88</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore.html">CompNovoIonScoringBase::IonScore</a> <a class="code" href="classOpenMS_1_1CompNovoIdentification.html#a7b7c9d2595dd3328e664293d3fec5ef9">IonScore</a>;</div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentification.html#a6cb23966d9741fbd0d2e87a1668042df">   89</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">CompNovoIdentificationBase::Permut</a> <a class="code" href="classOpenMS_1_1CompNovoIdentification.html#a6cb23966d9741fbd0d2e87a1668042df">Permut</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;    <span class="keywordtype">void</span> getDecompositionsDAC_(std::set&lt;String&gt; &amp; sequences, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> left, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> right, <a class="code" href="classdouble.html">DoubleReal</a> peptide_weight, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; CID_orig_spec, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; ETD_orig_spec, <a class="code" href="classOpenMS_1_1Map.html">Map&lt;DoubleReal, IonScore&gt;</a> &amp; CID_nodes);</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    <span class="keywordtype">void</span> reducePermuts_(std::set&lt;String&gt; &amp; permuts, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; CID_orig_spec, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; ETD_orig_spec, <a class="code" href="classdouble.html">DoubleReal</a> prefix, <a class="code" href="classdouble.html">DoubleReal</a> suffix);</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    <span class="keywordtype">void</span> getETDSpectrum_(<a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; spec, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp;sequence, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <span class="comment">/* charge */</span>, <a class="code" href="classdouble.html">DoubleReal</a> prefix = 0.0, <a class="code" href="classdouble.html">DoubleReal</a> suffix = 0.0);</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> estimatePrecursorWeight_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; ETD_spec, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp; charge);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;  };</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;}</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="CompNovoIdentificationBase_8h_html"><div class="ttname"><a href="CompNovoIdentificationBase_8h.html">CompNovoIdentificationBase.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt; Peak1D &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentification_html_a6cb23966d9741fbd0d2e87a1668042df"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentification.html#a6cb23966d9741fbd0d2e87a1668042df">OpenMS::CompNovoIdentification::Permut</a></div><div class="ttdeci">CompNovoIdentificationBase::Permut Permut</div><div class="ttdef"><b>Definition:</b> CompNovoIdentification.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentification_html_acc1a3401cf6077f8a9625b25b51e0731"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentification.html#acc1a3401cf6077f8a9625b25b51e0731">OpenMS::CompNovoIdentification::IsotopeType</a></div><div class="ttdeci">CompNovoIonScoringBase::IsotopeType IsotopeType</div><div class="ttdef"><b>Definition:</b> CompNovoIdentification.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment&lt; Peak1D &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html">OpenMS::CompNovoIdentificationBase</a></div><div class="ttdoc">run with CompNovoIdentificationBase </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:58</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIonScoringBase_html_af7e67702d51d0eff4c3db8ea8763a59f"><div class="ttname"><a href="classOpenMS_1_1CompNovoIonScoringBase.html#af7e67702d51d0eff4c3db8ea8763a59f">OpenMS::CompNovoIonScoringBase::IsotopeType</a></div><div class="ttdeci">IsotopeType</div><div class="ttdef"><b>Definition:</b> CompNovoIonScoringBase.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentification_html_a7b7c9d2595dd3328e664293d3fec5ef9"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentification.html#a7b7c9d2595dd3328e664293d3fec5ef9">OpenMS::CompNovoIdentification::IonScore</a></div><div class="ttdeci">CompNovoIonScoringBase::IonScore IonScore</div><div class="ttdef"><b>Definition:</b> CompNovoIdentification.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentification_html"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentification.html">OpenMS::CompNovoIdentification</a></div><div class="ttdoc">run with CompNovoIdentification </div><div class="ttdef"><b>Definition:</b> CompNovoIdentification.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">OpenMS::CompNovoIdentificationBase::Permut</a></div><div class="ttdoc">Simple class to store permutations and a score. </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:186</div></div>
<div class="ttc" id="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore_html"><div class="ttname"><a href="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore.html">OpenMS::CompNovoIonScoringBase::IonScore</a></div><div class="ttdef"><b>Definition:</b> CompNovoIonScoringBase.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html">OpenMS::PeptideIdentification</a></div><div class="ttdoc">Represents the peptide hits for a spectrum. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:63</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:12 using doxygen 1.8.5</font></TD>
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